The CompBio Lab

People

Anna Ritz (PI)
I joined the Reed College Biology Department in the Fall of 2015. For more information, see the home page, my CV, or the links on the right-side banner.
Current Members
Ibrahim Youssef, postdoctoral researcher
Ramin Neshati, visiting scholar
Zachary Campbell '18 summer research
Nick Egan '19 summer research
Yurel Watson '19 summer research
Giorlando Ramirez '20 summer research
Past Members
Thesis: Barney Potter '16, Heather Milne '16, Nicole Ezell '16, Nick Franzese '17, Moira Differding '17
Summer Research: Karl Menzel '17
Independent Studies: Alex Ledger '16, Karl Menzel '17, Danny Heinz '17

Summer 2017 Hike

2017 Hike up Hamilton Mountain with Suzy Renn's group and other students (we're tiny!).

Spring 2016 Thesis Students

2016 Thesis student photo! From left to right: Heather Milne, Nicole Ezell, Barney Potter, and Anna Ritz.

The CompBio Lab

Located in Biology B203, the Computational Biology (CompBio) lab is a resource for Biology students working on computationally-intensive research and thesis projects.

The new B203

The lab (shown here in October 2015) now includes machines and a printer, in addition to the large display and whiteboard.

Machines

B203 houses eight Linux computers (quad Intel Core i7-4790 processors with 16GB memory and 256GB solid state hard drives, purchased July 2015).

Students using the CompBio Lab will become familiar with unix-like environments and working from a terminal. Here are some places to get started.

  • Reed's Computer User Services has a Unix help page with many common commands and tips.
  • This amazing command-line bootcamp walks people through tutorials, all within a web browser.
  • There are many nice command-line tools for manipulating text files.
    • grep for matching strings and patterns in text.
    • awk for rearranging columns of text.
    • sed for searching and replacing strings and patterns in text.
  • Use top to see the processes currently running on your machine.
  • To see the size of a file (or files in a directory), use ls:

    ls -lh
  • To see the size of the contents of an entire directory (e.g., mydir), use du:

    du -h --max-depth 1 mydir

Access

B203 requires key-card access. By default, all of my thesis students will get access. If you are working on a computationally-intensive project, talk to me to see if it's appropriate for CompBio Lab use.

Use your username and password to log onto the machines. Just like the computer labs in the ETC, any files saved on the local machine are erased when you log out. Use file storage systems such as AFS or Google Drive to save your work (check out Sharing at Reed for a list of options. Save early, save often. Talk to me if you begin working with very large files that make this prohibitive.

You may choose to manage your projects with a versioning system such as GIT or SVN. GitHub is a popular place for hosting and managing projects (though they have a maximum upload size limit so storing data on GitHub is not ideal).

Remote Access

The machines can be remotely accessed when students are off campus. Only students with swipe access can remotely log into the machines. The machines are labeled bioinf1 to bioinf8.

You must first fill out a Virtual Private Network (VPN) request form, available on the VPN Policy Page. If you want to use your personal laptop for remote access, you may need to take extra security measures in order for Computer & Information Services to grant you access.

To log into a particular machine (e.g., bioinf5), you can ssh with

ssh username@bioinf5.reed.edu

where username is your Reed login. You will be prompted for your password.

Installed Packages

To request other software, email me with the name and download page. After I check the license, I will pass it on to Computer User Services and it will be installed on the machines within a couple days. To request Python modules or R packages, simply give me the module/package name.

Software:
blasr
Long read aligner designed for data sequenced by Pacific Biosciences (PacBio). [use cases]
blat
BLAST-like alignment tool. [user guide]
ncbi-blast+
Suite of Basic Local Alignment Search Tools (BLAST). [user manual]
synapseclient
Provides an interface to Synapse, a collaborative platform for data-intensive computational biology projects. [Python client]
inkscape
Free and open-source vector graphics editor (think Adobe Illustrator without the price tag). [tutorials]
samtools
Utilities for the Sequence Alignment/Map (SAM) format. [manpage]
Python modules:
matplotlib
A 2D plotting library. [gallery with source code]
networkx
A software package for the creation, manipulation, and study of networks. [tutorial]
R packages:
adgenet
Multivariate Analysis of Genetic Markers. [reference manual]
ape
Analyses of Phylogenetics and Evolution. [reference manual]
Rsamtools
Utilities for Sequence Alignment (R package). [documentation]

Spotted in the Lab

The Lab Wish List. The CompBio Lab is new and relatively sparse. If something is lacking, please let me know. Requests with a bit of thought and research may be taken more seriously.

Fall 2015 requests

For more images, see the blog post tag.

ritz portrait

Contact

Biology Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

Email aritz-at-reed-dot-edu

CV Curriculum Vitae [pdf]

Google Scholar Google Scholar
LinkedIn LinkedIn
Research Gate Research Gate
orcid ORCID iD
GitHub GitHub
WordPress Ritz Bits
WordPress Compbio Blog